Novel topoisomerase IV, corresponding nucleotide sequences and uses thereof

ABSTRACT

The present invention generally relates to a novel topoisomerase IV, the nucleotide sequences encoding this enzyme, their corresponding vectors, and the use of this enzyme for screening biologically active products.

[0001] The present invention relates to a novel topoisomerase IV, the nucleotide sequences encoding this enzyme, their corresponding vectors and the use of this enzyme for screening biologically active products.

[0002] Topoisomerases are enzymes capable of modifying the topological configuration of DNA rings, of making knots therein or of interlacing separated rings. They are thus involved in the replication, transcription and recombination of the entire genetic information (Wang et al., 1990). The mechanism of all these topological conversions is the same: the ring is opened so that a segment of DNA passes through the gap before the ends are rejoined. Two types of topoisomerase are involved in these conversions: type I topoisomerases which cut a single DNA strand and type II topoisomerases which cut both strands simultaneously.

[0003] Up until now, two type II bacterial topoisomerases have been identified and studied more particularly: gyrase from Escherichia coli (Gellert et al., 1976), and more recently, DNA topoisomerase IV from E.coli (Kato et al., 1990).

[0004] Gyras is a α₂β₂ tetramer whose a or GyrA and β or GyrB subunits are encoded by the gyrA and gyrB genes respectively. Bacterial gyrases are the only known topoisomerases capable of supercoiling relaxed DNA rings in the presence of ATP.

[0005] As regards more particularly DNA topoisomerase IV from E.coli, it relaxes supercoiled plasmid DNA, unknots T4 phage DNA and unwinds (or decatenates) kinetoplast DNA (Kato et al., 1992; Peng et al., 1993). The sequence of its corresponding genes, parC and parE from E.coli, has made it possible to demonstrate regions of high similarity between the subunits of gyrase and those of this topoisomerase IV, ParC with GyrA (35.6% over the entire sequence) and ParE with GyrB (40.1% over the entire sequence) respectively (Kato et al., 1990).

[0006]E.coli gyrase has also been identified as being a primary target of fluoroquinolones (Hooper et al., 1993). It has thus been demonstrated that E.coli strains mutated at the level of the Ser83 residue in the GyrA subunit have a high resistance to fluoroquinolones (Maxwell, 1992). Fluoroquinolones bind less to DNA-mutated gyrase complexes than to DNA-wild-type gyrase complexes. Indeed, other point mutations, mapped in the region between residues 67 and 106 of GyrA, lead to strains resistant to fluoroquinolones. This region is called QRDR (Yoshida et al., 1990; Cullen et al., 1989). Similar results have been published with strains of Staphylococcus aureus resistant to fluoroquinolones (Goswitz et al., 1992; Sreedharan et al., 1990). Gyrase is therefore nowadays recognized as being the primary target of quinolones. However, a clinical strain of Staphylococcus aureus, not containing any mutation in the QRDR region of GyrA, has also been described as resistant to fluoroquinolones (Sreedharan et al., 1991).

[0007] Nowadays, this phenomenon of resistance developed by Staphylococcus aureus bacteria towards antibiotics and more particularly towards fluoroquinolones is being increasingly encountered at the therapeutic level. It would be particularly important to be able to lift this resistance and this involves a characterization of all the parameters which are associated with it.

[0008] The main objective of the present invention is precisely the identification, sequencing and characterization of nucleic sequences encoding subunits of a novel topoisomerase, topoisomerase IV of Staphylococcus aureus, composed of two subunits, GrlA and GrlB.

[0009] Unexpectedly, the applicant has found that the primary target of the fluoroquinolones in S. aureus is a topoisomerase IV and not gyrase. It has thus demonstrated that clinical strains of S. aureus, in which the QRDR region of the GyrA subunit of gyrase is identical to th wild-type sequence, develop nevertheless a resistance to fluoroquinolones because of a mutation which they possess in the region of the GrlA subunit of topoisomerase IV, homologous to the QRDR region.

[0010] The first subject of the present invention is a nucleotide sequence encoding at least one subunit of topoisomerase IV of Staphylococcus aureus.

[0011] The present invention describes in particular the isolation and the characterization of the grlA and grlB genes. These genes have been cloned, sequenced and expressed in E. coli, and their enzymatic activity has been characterized. They were isolated from a Staphylococcus aureus genomic DNA library. From the grlAB nucleic sequence (SEQ ID No. 1), two open frames, corresponding to the grlB and grlA genes respectively, have been identified. The grlA and grlB genes have been sequenced in SEQ ID No. 2 and SEQ ID No. 3 respectively.

[0012] Preferably, the subject of the present invention is a nucleotide sequence chosen from:

[0013] (a) all or part of the grlA (SEQ ID No. 2) or grlB (SEQ ID No. 3) genes,

[0014] (b) the sequences hybridizing with all or part of the (a) genes and encoding a subunit of a topoisomerase IV, and

[0015] (c) the sequences derived from the (a) and (b) sequences because of the degeneracy of the genetic code.

[0016] It is clear that from the genes identified in the present application, it is possible, by hybridization, to directly clone other genes encoding a subunit of topoisomerase IV of bacteria close to S. aureus such as for example Streptococci and Enterococci. It is thus possible to clone this type of gene using, as probe, the genes grlA, grlB or fragments thereof. Likewise, the cloning of these genes may be carried out using degenerate oligonucleotides derived from sequences of the grlA or grlB genes or fragments thereof.

[0017] For the purposes of the present invention, derivative is understood to mean any sequence obtained by one or more modifications and encoding a product conserving at least one of the biological properties of the original protein. Modification should be understood to mean any mutation, substitution, deletion, addition or modification of a genetic and/or chemical nature. These modifications may be performed by techniques known to persons skilled in the art.

[0018] Among the preferred derivatives, there may be mentioned more particularly natural variants, molecules in which one or more residues have been substituted, derivatives obtained by deletion(s) of regions not or little involved in the interaction between the binding sites considered or expressing an undesirable activity, and derivatives having, compared with the native sequence, one or more additional residues.

[0019] Still more preferably, the subject of the invention is the nucleotide sequences represented by the grlA (SEQ ID No. 2) and grlB (SEQ ID No. 3) genes.

[0020] It also relates to any grlA gene having a mutation leading to a resistance to molecules of the quinolone and more particularly of the fluoroquinolone family. As a representative of these mutated genes, there may be mentioned more particularly the grlA gene having a base change from C to A at position 2270 of SEQ ID No. 2. The resulting gene is termed grlA_((c-2270A)). This mutation leads to substitution of the Ser-80 residue with Tyr in the GrlA protein. The resulting protein will be designated by GrlA_((Ser-80 Tyr)).

[0021] Another subject of the present invention relates to a recombinant DNA comprising at least one nucleotide sequence encoding a subunit of topoisomerase IV of Staphylococcus aureus. More preferably, it is a recombinant DNA comprising at least one nucleotide sequence as defined above in (a), (b) and (c) and more particularly the gene grlA (SEQ ID No. 2) grlA _((C-2270A)) and/or the gene grlB (SEQ ID No. 3).

[0022] According to a preferred mode of the invention, the nucleotide sequences defined above form part of an expression vector which may be autonomously replicating or integrative.

[0023] Another subject of the invention relates to the polypeptides resulting from the expression of the nucleotide sequences as defined above. More particularly, the present invention relates to the polypeptides comprising all or part of the polypeptides GrlA (SEQ ID No. 2) or GrlB (SEQ ID No. 3) or of their derivatives. For the purposes of the present invention, the term derivative designates any molecule obtained by modification of the genetic and/or chemical nature of the peptide sequence. Modification of the genetic and/or chemical nature may be understood to mean any mutation, substitution, deletion, addition and/or modification of one or more residues. Such derivatives may be generated for different purposes, such as especially that of increasing the affinity of the peptide for its substrate(s), that of enhancing its production levels, that of increasing its resistance to proteases, that of increasing and/or of modifying its activity, or that of conferring new biological properties on it. Among the derivatives resulting from an addition, there may be mentioned, for example, the chimeric polypeptides containing an additional heterologous part attached to one end. The term derivative also comprises the polypeptides homologous to the polypeptides described in the present invention, derived from other cellular sources.

[0024] Preferably, they are the polypeptides GrlA (SEQ ID No. 2), GrlB (SEQ ID No. 3) and GrlA_((Ser-80Tyr)). The subject of the invention is also any recombinant cell containing a nucleotide sequence, a recombinant DNA and/or a vector as defined above. The recombinant cells according to the inv ntion may be both eukaryotic and prokaryotic cells. Among the suitable eukaryotic cells, there may be mentioned animal cells, yeasts, or fungi. In particular, as regards yeasts, there may be mentioned yeasts of the genus Saccharomyces, Kluyveromyces, Pichia, Schwanniomyces or Hansenula. As regards animal cells, there may be mentioned COS, CHO and C127 cells, Xenopus eggs, and the like. Among the fungi, there may be mentioned more particularly Micromonospora, Asperaillus ssp. or Trichoderma ssp. Preferably, they are prokaryotic cells. In this case, the following bacteria may be more particularly used: Actinomycetes, Bacillus, and more preferably E. coli and Staphylococcus. The recombinant cells of the invention may be obtained by any method allowing the introduction of a foreign nucleotide sequence into a cell. This may be especially transformation, electroporation, conjugation, fusion of protoplasts, or any other technique known to persons skilled in the art.

[0025] The subject of the present invention is also a process for the preparation of polypeptides as claimed from the culture of one of these recombinant cells. The polypeptide(s) thus obtained are recovered according to conventional methods after the culture.

[0026] The invention also relates to an isolated topoisomerase IV capable of being obtained from the expression of all or part of the grlA gene (SEQ ID No. 2) and of all or part of the grlB gene (SEQ ID No. 3) or of their respective derivatives.

[0027] Derivative is understood to designate the sequences hybridizing with all or part of the grlA or grlB gene and encoding a subunit of a topoisomerase IV as well as all the sequences derived from a degeneracy of the genetic code of these hybrid sequences or of the sequences corresponding to all or part of the grlA or grlB gene.

[0028] More preferably, it is an isolated topoisomerase IV derived from the expression of all or part of the grlA gene (SEQ ID No. 2) or of all or part of the grlB gene (SEQ ID No. 3).

[0029] The present invention relates more particularly to any topoisomerase IV behaving as a primary target towards fluoroquinolones.

[0030] According to a specific mode of the invention, it is topoisomerase IV of Staphylococcus aureus.

[0031] The claimed topoisomerase IV according to the invention is most particularly useful for targeting biologically active products such as for example potential antibiotics and especially molecules of the fluoroquinolone family. Advantageously, it may also be used to assay and/or identify products inhibiting the ATP-dependent DNA relaxing reaction and/or the products inhibiting the reaction of decatenation of catenanes of DNA.

[0032] The applicant has thus developed an assay for enzymatic activity which is specific for topoisomerase IV of S. aureus and has shown that this activity is inhibited by antibiotic molecules such as fluoroquinolones.

[0033] The present invention provides a new target for searching for new antibiotics, as well as a screen specific for this target; this screen is described in Example 7. This screen makes it possible to demonstrate the products which inhibit DNA topoisomerase IV of S. aureus. The following may be used in this test: pure or mixed synthetic products, natural plant extracts, bacterial cultures, fungi, yeasts or algae, pure or in the form of a mixture. The test described in the present invention makes it possible to detect both products which stabilize the cleavable complex, a reaction intermediate of the reaction catalysed by the enzyme, and also inhibitors acting through other mechanisms.

[0034] The examples and figures presented below by way of nonlimiting illustration show other advantages and characteristics of the present invention.

LEGEND TO THE FIGURES

[0035]FIG. 1: Restriction map of the 4565 bp fragment containing the grlB and grlA genes of S. aureus.

[0036]FIG. 2: Construction of the plasmids for expression of grlA and grlB. The constructs produced with grlA are schematically represented in A and those of grlB are in B. The cloned S. aureus DNA is represented by the shaded rectangles, the vectors derived from M13 are in thick black line and the expression vectors are in a fine black line, the SstI restriction site is in brackets because it is a cloning site.

[0037]FIG. 3: PAGE-SDS electrophoresis gel stained with Coomasie blue. Total cell extracts are deposited, lanes: 1 and 2, XL1-blue, pXL2340; 3 and 4, XL1-blue, pRSETB; 5 and 6, XL1-blue, pXL2320. The molecular weight markers (in hundreds) are indicated on the right of the figure. The arrow shows the overproduced protein. The + or − signs represent the induction with or without IPTG.

[0038]FIG. 4: ATP-dependent relaxation activity of the GrlAB protein. The control experiments with purified DNA topoisomerase IV of E. coli (Peng and Marians, 1993) and purified DNA gyrase of E. coli (Hallet et al., 1990) are also described.

[0039]FIG. 5: Decatenation activity of the protein GrlAB. kDNA, kinetoplast DNA; monomers, relaxed and decatenated DNA monomers. TopoIV: purified DNA topoisomerase IV of E. coli (50 ng); Gyrase: purified DNA gyrase of E. coli (50 ng); GrlA: GrlA protein extract (2 μg); GrlB: GrlB protein extract (2 μg); GrlAB: GrlA protein extract (2 μg) mixed with the GrlB protein extract (2 μg).

EXAMPLE 1 PCR amplification of DNA Fragments of Staphylococcus aureus Which are Inside the grlA and grlB Genes

[0040] This example describes the production of DNA fragments of Staphylococcus aureus which are inside the grlA and grlB genes. These fragments were obtained after PCR amplification carried out at 50° C. with genomic DNA of the Staphylococcus aureus strain RN4220 (Novick, 1990) and of the degenerate oligonucleotides corresponding to the amino acids conserved in the N-terminal regions of the subunits GyrA of E. coli and B. subtilis and ParC of E. coli or of the subunits GyrB of E. coli and B. subtilis and ParE of E. coli. More specifically, the sense oligonucleotides 2137 and antisense oligonucleotides 2135 made it possible to amplify fragments of 255 bp which can encode 85 amino acids which would correspond to positions 39 to 124 on the E. coli GyrA sequence; the sequence of the sense oligonucleotide 2137 is 5′-GCGCGAATTCGATGG(A,T)(C,T)T(A,T)AAACC(A,T)GT(A,T)CA-3′ (SEQ ID No. 4) and that of the antisense 2135 is 5′-CGCGAAGCTTTTC(T,A)GTATA(A,T)C(T,G)CAT(A,T)GC(A,T)GC-3′ (SEQ ID No. 5). The oligonucleotides 2144 and 2138 led to the amplification of 1 kb fragments which can encode 333 amino acids which would correspond to positions 98 to 430 on the E. coli GyrB sequence; the sequence of the sense oligonucleotide 2144 is 5′-GCGCGAATTCT(T,A)CATGC(A,T)GG(T,A)GG(T,A)AAATT-3′ (SEQ ID No. 6), and that of the antisense 2138 is 5′-CGCGAAGCTT(T,A)CC(T,A)CC(T,A)GC(T,A)GAATC(T,A)CCTTC-3′ (SEQ ID No. 7) . The fragments were cloned and a total of 40 clones were analysed by sequencing their insert. The sequence of the oligonucleotides used for the PCR was found for 31 clones out of 40; among the 31 clones, 20 have a sequence which is inside the gyrA or gyrB gene of S. aureus; the other 11 clones contain either a fragment A of 255 bp or a fragment B of 1 kb.

[0041] The amino acid sequence which the A fragment is thought to encode has 59% identity with the GyrA subunit of S. aureus between positions 44 to 125, the A fragment is therefore thought to be part of an S. aureus grlA gene thus newly identified. Likewise, the amino acid sequence which the B fragment is thought to encode has 51% identity with the GyrB subunit of S. aureus between positions 105 to 277, the B fragment is therefore thought to be part of an S. aureus grlB gene thus newly identified.

EXAMPLE 2 Cloning and Sequencing of the grlA and grlB Genes of Staphylococcus aureus

[0042] This example describes the molecular biology experiments which have made it possible to clone and then sequence the grlA and grlB genes of Staphylococcus aureus.

[0043] The A and B fragments described in Example 1 were used as radioactive probe to identify, by hybridization, the grlA and grlB genes in a genomic DNA library of S. aureus FDA 574 (CE ent⁺) constructed in λgt11 by Clontech Laboratories (catalogue XL1501b, batch 0721). Out of a total of 250,000 recombinant phages, twelve phages hybridize with the A fragment or the B fragment but do not hybridize with oligonucleotides specific for the gyrA or gyrB genes. The size of the EcoRI inserts contained in these phages varies between 0.7 and 3.5 kb and two phages, 16 and 111, whose insert is of a larger size, were studied. The EcoR1 insert of 3.5 kb of the phage 16 was eluted and then digested with XbaI and the two fragments of 1.5 and 2 kb were cloned into M13mp19 and M13mp18 (Boehringer Mannheim) in order to generate pXL2321 and pXL2322. Likewise, the EcoRI insert of 3.6 kb of the phase 111 was eluted and then digested with PstI and the 2 kb fragment was cloned into M13mp19 in order to generate pXL2324.

[0044] The inserts contained in the recombinant phages pXL2321, pXL2322 and pXL2324 were sequenced on both strands with the aid of the universal primer or of internal oligonucleotides using the Sanger method. The nucleic sequence grlAB (SEQ ID No. 1) of 4565 bp was analysed with the programme by Staden et al., 1982 in order to identify the coding sequences with the aid of a codon usage table for S. aureus. Only two open frames ORF1 (positions 41 to 2029) and ORF2 (positions 2032 to 4431) wer thus determined. On SEQ ID No. 1, the coding strand is th 5′->3′ top strand, the open frame ORF1 starts arbitrarily at ATG position 41 but it can also start at TTG position 17 or 35, this codon being already described as initiation codon in S. aureus; the stop codon of ORF1 overlaps with the initiation codon GTG of ORF2, which is characteristic of a translational coupling (Normark et al., 1983); such a coupling has, for example, been described for the gyrA and gyrB genes of Haloferax sp. (Holmes et al., 1991). These open frames have a percentage of GC of 34.5% which is a value in agreement with the values described for the S. aureus DNA in the literature (Novick, 1990). Moreover, the B fragment is identical to the sequence described on SEQ ID No. 1 from position 333 to position 1348 in ORF1 and the fragment A is identical to the sequence of SEQ ID No. 1 from position 2137 to position 2394 in ORF2. From the nucleotide sequence, a restriction map is produced with enzymes which cut least frequently, see FIG. 1.

[0045] This sequence analysis shows that ORF1 is the grlB gene and ORF2 the grlA gene.

EXAMPLE 3 Primary Structure, Expression and Function of the GrlA and GrlB Proteins Encoded by the grlA and grlB genes of Staphylococcus aureus

[0046] This example describes the primary structure, the expression in E. coli and the function of the GrlA and GrlB proteins of Staphylococcus aureus. This function, which corresponds to a DNA topoisom rase IV, is based, in this example, on sequence homology and genetic complementation data.

[0047] 3.1—Primary Structure and Sequence Analysis of the GrlA and GrlB Proteins

[0048] This example describes computer analysis of the sequence of the grlA and grlB genes of Staphylococcus aureus carried out using the sequence data presented in Example 2. The grlB gene encodes a GrlB protein of 663 amino acids (molecular weight 74,318), and the grlA gene encodes a GrlA protein of 800 amino acids (molecular weight 91,040). The coding parts of the grlB and grlA genes, the sequences of the GrlB and GrlA proteins are presented in SEQ ID No. 3 and SEQ ID No. 2 respectively and the properties of each of these proteins (amino acid composition, isoelectric point, polarity index) are presented in Tables 1 and 2 below. TABLE 1 Protein: GrlA: First residue = 1 and last residue = 800 Molecular mass (monoisotopic) = 91040.8438 Molecular mass (average) = 91097.2578 Polarity ind x (%) = 52.00 Iso lectric point = 6.77 OD 260 (1 mg/ml) = 0.298 OD 280 (1 mg/ml) = 0.487 NUMBER % NOMB WEIGHT % WEIGHT  1 Phe F 22 2.75 3235.51 3.55  2 Leu L 74 9.25 8368.22 9.19  3 Ile I 77 9.63 8707.47 9.56  4 Met M 19 2.38 2489.77 2.73  5 Val V 59 7.38 5845.04 6.42  6 Ser S 51 6.38 4438.63 4.88  7 Pro P 22 2.75 2135.16 2.35  8 Thr T 43 5.38 4345.05 4.77  9 Ala A 37 4.63 2628.37 2.89 10 Tyr Y 28 3.50 4565.77 5.02 12 His H 20 2.50 2741.18 3.01 13 Gln Q 26 3.25 3329.52 3.66 14 sn N 45 5.63 5131.93 5.64 15 Lys K 66 8.25 8454.27 9.29 16 Asp D 54 6.75 6211.45 6.82 17 Glu E 67 8.38 8645.85 9.50 18 Cys C  0 0.00   0.00 0.00 19 Trp W  2 0.25  372.16 0.41 20 Arg R 44 5.50 6868.45 7.54 21 Gly G 44 5.50 2508.94 2.76

[0049] TABLE 2 GrlB protein: First residue = 1 and last residue = 663 Molecular mass (monoisotropic) = 74318.3516 Molecular mass (average) = 74363.9219 Polarity ind x (%) = 53.70 Iso lectric point = 7.21 OD 260 (1 mg/ml) = 0.404 OD 280 (1 mg/ml) = 0.603 NUMBER % NOMB WEIGHT % WEIGHT  1 Phe F 26 3.92 3823.78 5.15  2 Leu L 55 8.30 6219.62 8.37  3 Ile I 36 5.43 4071.03 5.48  4 Met M 10 1.51 1310.40 1.76  5 Val V 50 7.54 4953.42 6.67  6 Ser S 41 6.18 3568.31 4.80  7 Pro P 15 2.26 1455.79 1.96  8 Thr T 41 6.18 4142.95 5.57  9 Ala A 33 4.98 2344.22 3.15 10 Tyr Y 19 2.87 3098.20 4.17 12 His H 14 2.11 1918.82 2.58 13 Gln Q 26 3.92 3329.52 4.48 14 Asn N 36 5.43 4105.55 5.52 15 Lys K 63 9.50 8069.98 10.86  16 Asp D 40 6.03 4601.08 6.19 17 Glu E 61 9.20 7871.60 10.59  18 Cys C  0 0.00   0.00 0.00 19 Trp W  4 0.60  744.32 1.00 20 Arg R 34 5.13 5307.44 7.14 21 Gly G 59 8.90 3364.27 4.53

[0050] The Kanehisa programme, described in 1984, was used to align the GrlB and GrlA proteins with the following type II bacterial DNA topoisomerases, the E. coli, B. subtilis or S. aureus gyrases or the E. coli topoisom rase IV. The degrees of identity, a Table 3, are high and are between 32 and 55%. More specifically, GrlB exhibits a greater degree of identity with the GyrB subunits of E. coli (49%) and of S. aureus (52%) than with ParE of E. coli (38%), whereas GrlA exhibits comparable degrees of identity with the GyrA subunits of E. coli (32%) and of S. aureus (39%) than with ParE of E. coli (33%).

[0051] The GyrB subunits of Staphylococcus aureus (Margerrison et al., 1992), Bacillus subtilis (Moriya et al., 1985), and Escherichia coli (Adachi et al., 1987) are called SAGYRB, BSGYRB and ECGYRB respectively, GrlB is called SAGRLB and ECPARE corresponds to ParE of E. coli (Kato et al., 1990). A similar nomenclature is used for the GyrA, GrlA and ParC subunits. The numbers under the name of the proteins are the numbers of amino acids in them. TABLE 3 B or B-like SAGYRB SAGRLB BSGYRB ECGYRB subunits 644 663 638 804 SAGRLB 52% BSGYRB 68% 55% ECGYRB 55% 49% 57% ECPARE 40% 38% 40% 40% A or A-like SAGYRA SAGRLA BSGYRA ECGYRA subunits 887 800 821 875 SAGRLA 39% BSGYRA 65% 40% ECGYRA 39% 32% 41% ECPARC 38% 33% 36% 32%

[0052] Multiple alignments between the type II bacterial topoisom rases, performed with the CLUSTAL programme of Higgins t al., 1988, show numerous conserved regions between the sequences of the various B, GrlB and ParE subunits and in the N-terminal part of the sequence of the A, GrlA and ParC subunits. The residues conserved in the N-terminal region of the B subunits of these proteins are in fact the residues involved in the binding of ATP and identified from X-ray crystallization data with the E. coli GyrB (Wigley et al., 1991). The residues conserved in the N-terminal region of the A subunits of these proteins are either the residues AAMRYTE (SEQ ID No. 8) close to the active site of gyrase Tyr-122, identified on the E. coli GyrA (Horowitz et al., 1987), or the residues YEPHGDS (SEQ ID No. 9) modified in the strains resistant to fluoroquinolones (Hooper et al., 1993).

[0053] 3.2—Expression of the grlA and grlB genes in E. coli.

[0054] This example describes the constructs produced in order to express, in E. coli, the grlA or grlB genes under the control of the pT7 promoter (Studier et al., 1990). The expression plasmid pXL2320, see FIG. 2, containing the grlB gene in the vector pRSETB (Studier et al., 1990; Invitrogen) was constructed by cloning 1) the 1 kb EcoRI-XbaI insert of pXL2321 into pXL2322 at the XbaI and EcoRI sites in order to gene rat pXL2323; 2) th 1.9 kb KpnI-EcoRI insert of pXL2323 at th KpnI and EcoRI sites of the vector pRSETB in order to gene rat pXL2319; the 0.5 kb NdeI-KpnI insert of pXL2325 at th NdeI and KpnI sites of pXL2319 in order to obtain pXL2320. (pXL2325 contains the first 500 bas s of the gene where a CAT sequence has been introduced by mutagenesis, just upstream of the ATG initiation codon, in order to create an NdeI site). The grlB gene expression cassette contained in pXL2320 was cloned at the BalI and EcoRI sites of pKT230 (Bagdasarian et al., 1981) in order to obtain pXL2439. The expression plasmid pXL2340, see FIG. 2, containing the grlA gene in the vector pRSETB was constructed by cloning 1) the 1.7 kb Ndel-EcoRI insert of pXL2324 at the NdeI and EcoRI sites of the vector pRSETB in order to generate pXL2338; the 0.75 kb NdeI insert of pXL2337 at the NdeI sites of pXL2338 in order to obtain pXL2340. (pXL2337 contains the first 750 bases of the gene where a CATATG sequence has been introduced by mutagenesis, in place of the GTG initiation codon in order to create an NdeI site).

[0055] The plasmids pXL2320, or pXL2340 were introduced into the E. coli XL-1-Blue strain (Stratagen) and the expression of the genes was induced when the T7 phage RNA polymerase was produced after induction of the gene, encoding the T7 phage RNA polymerase, cloned into the helper phage M13/T7 (Studier et al., 1990, Invitrogen). The cellular extracts were analysed by electrophoresis on a PAGE-SDS gel stained with Coomasie blue as has already been described (Denèfle et al., 1987). In FIG. 3 is represented the production of a protein with a i) molecular weight of 79,000, when the grlB gene is induced in the E. coli strain XL1-blue, pXL2320; and ii) molecular weight of 90,000, when the grlA gene is induced in the E. coli strain XL1-Blue, pXL2340. The measured molecular weights are in agreement with the molecular weights deduced from the sequence.

[0056] 3.3—Complementation of the parCts and parEts Mutants of Salmonella typhimurium by the grlA and grlB Genes of Staphylococcus aureus

[0057] This example describes the heterologous complementation of the S. typhimurium parCts and parEts mutants by the S. aureus grlA and grlB genes. The plasmids pXL2320, pXL2340, pXL2439 or the vector pRSETB were introduced into the S. typhimurium strains SE7784 (parC281(Ts) zge-2393::Tn10 leu485) or SE8041 (parE206(Ts) zge-2393::Tn10 leu485) (Luttinger et al., 1991). No plasmid complements the heat-sensitive phenotype; on the other hand, when the plasmids pXL2340 and pXL2439 are introduced simultaneously into the SE7784 strain or into the SE8041 strain, the heat-sensitive phenotype of both strains is complemented. Consequently, the coexpression of the grlA and grlB genes of S. aureus allows the complementation of the ParC Ts or ParE Ts phenotype of the S. typhimurium mutants.

EXAMPLE 4 The DNA Topoisomerase IV of S. aureus is the Primary Target of the Fluoroquinolones

[0058] This example describes the presence of a point mutation Ser-80 in the GrlA subunit with all the analysed clinical strains of S. aureus resistant to the fluoroquinolones whereas a mutation in the QRDR region (Quinolone Determining Region) (equivalent to the Ser-80 region of GrlA) in the GyrA subunit does not exist with the clinical strains of S. aureus weakly resistant to the fluoroquinolones. Consequently, the GrlA subunit is shown to be the primary target of the fluoroquinolones in S. aureus.

[0059] The genomic DNA of eight clinical strains of S. aureus and of a laboratory strain was prepared and used to amplify at 42° C. by PCR: i) the first 500 base pairs of gyrA using the sense oligonucleotide 5′-GGCGGATCCCATATGGCTGAATTACCTCA-3′ (SEQ ID No. 10) and the antisense oligonucleotide 5′-GGCGGAAT TCGACGGCTCTCTTTCATTAC-3′ (SEQ ID No. 11); ii) and the first 800 base pairs of grlA using the sense oligonucleotide 5′-GGCCGGATCCCATATGAGTGAAATAATTCAAGATT-3′ (SEQ ID No. 12) and the antisense oligonucleotide 5′-GGCCGAATTCTAATAATTAACTGTTTACGTCC-3′ (SEQ ID No. 13). Each amplified fragment was cloned into the phage M13mp18 and the sequence of the first 300 base pairs of ach of the genes was read n 2 clones. The gyrA sequence is identical to that published by Magerrison and that of grlA to that described in SEQ ID No. 1, with the exception of the mutations presented in Table 4. The mutations in gyrA exist with the strains highly resistant to fluoroquinolones (SA4, SA5, SA6, SA35, SA42R and SA47; MIC for ciprofloxacin >16 mg/l); these mutations are a base change which leads to changes in the amino acids Ser-84 or Ser-85 or Glu-88. A mutation in grlA exists with all the strains resistant to fluoroquinolones and corresponds to the changing of the residue Ser-80 to Phe or Tyr. TABLE 4 MIC mg/l Mutation in gyrA Mutation in grlA Strain Ciprofloxacin Base Codon Base Codon RN4220* 1 no no no no SA42* 0.5 no no no no SAH** 2 no no 2281 ⁸⁴Glu->Lys G->A SA1* 2 no no 2270 ⁸⁰Ser->Phe C->T SAA** 4 no no 2281 ⁸⁴Glu->-Lys G->A SA3** 4 no no 2270 ⁸⁰Ser->Phe C->T SA2** 16 no no 2270 ⁸⁰Ser->Tyr C->A SA47* 16 2533 ⁸⁴Ser->Leu 2270 ⁸⁰Ser->Tyr C->T* C->A SA4** 32 2544 ⁸⁸Glu->Lys 2270 ⁸⁰Ser->Phe G->A C->T SA5** 32 2533 ⁸⁴Ser->Leu 2270 ⁸⁰Ser->Phe C->T C->T SA6** 32 2533 ⁸⁴Ser->Leu 2270 ⁸⁰Ser->Phe C->T C->T SA35* 64 2535 ⁸⁵Ser->Pro 2270 ⁸⁰Ser->Tyr T->C C->A SA42R* >128 2533 ⁸⁴Ser->Leu 2270 ⁸⁰Ser->Tyr C->T* C->A

EXAMPLE 5 PCR (Polymerase Chain Reaction) Amplification of the S. aureus DNA Fragment Which is Inside grlA Containing a Point Mutation Which Leads to a Substitution in GrlA from Ser-80 to Tyr (Ser-80→Tyr)

[0060] This example describes the production of the DNA fragment which is inside grlA of an S. aureus strain, SA2, resistant to fluoroquinolones. The grlA fragment contains a base change from C to A at position 2270 of the wild-type gene (FIG. 1). This mutation leads to a substitution of the residue S r-80 to Tyr in the GrlA protein. It has been shown that a substitution of the residue Ser-80 to Phe or Tyr exists with all the strains weakly resistant to fluoroquinolones (Example 4). The fragment which is inside grlA was obtained after PCR amplification carried out at 50° C. with the genomic DNA of the SA2 strain and of the oligonucleotides 3358 and 3357 which correspond to position 2036 and 3435 respectively on the sequence of grlA. More specifically, the sense oligonucleotide 3358 (SEQ ID No. 12) (Example 4) and the antisense oligonucleotide 3357 made it possible to amplify a fragment of 1399 base pairs; the sequence of the antisense oligonucleotide 3357 is 5′-GGCCGAGCTCCAATTCTTCTTTTATGACATTC-3′ (SEQ ID No. 14). The oligonucleotide 3358 was also used to introduce, by mutagenesis, a sequence CATATG, in place of the GTG initiation codon in order to create an NdeI site. The amplified grlA fragment was cloned into the BamHI/SstI cloning sites of pUC18 (Boehringer Mannheim), and 6 clones containing this plasmid, pXL2692, were analysed after sequencing their insert. In all cases, a sequence CATATG was introduced in place of the CTG initiation codon, and the point mutation at position 2270 of grlA (C→A) was again found.

EXAMPLE 6 Expression in E. coli of the grlA Gene Containing a Base Change Corresponding to the Change of the Residue Ser-80 to Tyr

[0061] This example describes the construct prepared in order to express, in E. coli, the mutated grlA gene under the control of the T7 promoter (Studier et al., 1990). The expression plasmid pXL2742, containing the mutated grlA gene, was constructed by cloning the 0.75 kb insert of pXL2692 into the NdeI site of pXL2338 (Example 3.2). The plasmid pXL2742 was introduced into the E. coli XL1-Blue strain and the expression of the grlA gene was carried out as described in Example 3.2. The production of a protein having a molecular weight of 90,000 was obtained with the plasmid pXL2742 containing the grlA gene. The molecular weight measured is in agreement with the molecular weight deduced from the sequence of the grlA gene, and that already obtained for the wild-type GrlA protein (Example 3.2).

EXAMPLE 7 DNA Topoisomerase IV Activity of the GrlAB Protein of S. aureus

[0062] This example illustrates how an acellular extract containing the GrlAB protein can be prepared and how the enzymatic activity of the GrlAB protein present in this extract can be detected and measured.

[0063] 7.1—Preparation of the Cell Extracts

[0064] An acellular extract of the E. coli strain XL1-blue pXL2340 expressing the GrlA protein is prepared for example in the following manner:

[0065] The E. coli strain XL1-blue pXL2340 is cultured as follows: 250 ml of LB medium containing ampicillin at 50 mg/l are inoculated at {fraction (1/100)} with a culture of E. coli XL1-blue pXL2340, and incubated at 30° C.; when the optical density at 600 nm is 0.3, 1 mM IPTG is added; after incubating for 30 min at 37° C., the strain is infected with the helper phage M13/T7 with a multiplicity of infection of 5 pfu per cell for 4 hours. After centrifugation (5000×g; 20 min), the cells obtained using 1.5 litres of culture are resuspended in 20 ml of 50 mM Tris/HCl buffer pH 7.8 containing 10 mM EDTA, 150 mM NaCl, 1 mM DTT, 0.12% Brij 58 and 0.75 mg/ml of lysozyme. After 30 min at 4° C., the mixture is centrifuged for 1 h at 50,000×g and the supernatant containing the GrlA protein is recovered. A change of buffer is carried out on this sample by chromatographing the extract through a column filled with Sephadex G625 (Pharmacia) equilibrated and eluted with the 50 mM Tris/HCl buffer pH 7.5 containing 1 mM EDTA, 5 mM DTT, 100 mM NaCl and 10% sucrose.

[0066] An acellular extract containing the GrlB protein is prepared in a similar manner using the E. coli strain XL1-blue pXL2320.

[0067] 7.2—Purification of the DKN Topoisom rase IV of S. aureus.

[0068] This example illustrates how an S. aureus enzyme catalysing the segregation of the daughter chromosomes during the final phase of replication (topoisomerase IV) can be purified.

[0069] The purification of the two GrlA and GrlB subunits of topoisomerase IV is carried out as described below, using the decatenation activity assay described in Example 7.3 to detect the presence of the GrlA and GrlB proteins during the purification, as is commonly used by persons skilled in the art. During the assay of this enzymatic activity, complamentation of the fractions containing the GrlA protein is obtained with 1 μg of proteins of an extract of the E. coli strain XL1-blue pXL2320 expressing the GrlB subunit, and complementation of the fraction containing the GrlB protein is obtained with 1 μg of proteins of an extract of the E. coli strain XL1-blue pXL2340 expressing the GrlA subunit. A preferred mode of preparation of the enzymatic extracts is described in Example 7.1. Between each stage, the fractions containing the desired protein are frozen and stored at −70° C. The purification of the A subunit may be carried out by chromatography, for example, according to the following procedure:

[0070] an acellular extract prepared as described in Example 7.1 using about 5 g of cells of E. coli XL1-blue pXL2340 is chromatographed on a MonoQ HR 10/10 column (Pharmacia) at a flow rate of 3 ml/min with a linear gradient of NaCl (0.1M to 0.6M over 60 min) in a 10 mM Tris/HCl buffer pH 8.0 containing 1 mM EDTA, 1 mM DTT and 10% glycerol (w/v). The active fractions are combined and the sample is chromatographed on a Superdex 200 HiLoad 26/60 column (Pharmacia) equilibrated and eluted with 50 mM Tris/HCl buffer pH 7.5 containing 1 mM EDTA, 5 M DTT and 0.25 M NaCl. The GrlA protein, which exists in the form of a symmetrical peak, is coeluted with the desired activity. After this stage, the preparation shows a single visible band in SDS-PAGE after developing with silver nitrate, and this band migrates with an apparent molecular weight of about 90,000.

[0071] The purification of the B subunit may be carried out by chromatography, for example, according to the following procedure:

[0072] an acellular extract prepared as described in Example 5 using about 5 g of cells of E. coli XL1-blue pXL2320 is injected onto a Novobiocin-Sepharose CL-6B column (6 ml of gel prepared according to the procedure described by Staudenbauer et al., 1981, Nucleic Acids Research) equilibrated in 50 mM Tris/HCl buffer pH 7.5 containing 1 mM EDTA, 5 mM DTT and 0.3 M NaCl. After washing the column with the same buffer, the GrlB protein is eluted with 50 mM Tris/HCl buffer pH 7.5 containing 1 mM EDTA, 5 mM DTT and 2 M NaCl and 5 M urea. This fraction is then chromatographed on a Superdex 200 HiLoad 26/60 gel permeation column (Pharmacia) equilibrated and eluted with 50 mM Tris/HCl buffer pH 7.5 containing 1 mM EDTA, 5 mM DTT and 0.25 M NaCl. The GrlB protein, which exists in the form of a symmetrical peak, is coeluted with the desired activity. After this stage, the preparation has a single visible band in SDS-PAGE after developing with silver nitrate, and this band migrates with an apparent molecular weight of about 80,000.

[0073] 7.3—Detection of the Enzymatic Activities of the GrlAB Protein.

[0074] The various enzymatic activities of the GrlAB protein are detected by incubating, in the same reaction mixture, equal quantities of the two types of extracts prepared by the process described above or by any other process which makes it possible to recover the intracellular enzymatic proteins of the microorganism while preserving their activity, such as for example the procedures involving the use of presses (such as the French Press, the X-Press), or the use of ultrasound.

[0075] The ATP-dependent supercoiled DNA relaxing activity can be detected by carrying out the procedure, for example, in the following manner:

[0076] a mixture of an extract of the E. coli strain XL1-blue pXL2320 (1 μg of proteins) and of an extract of the E. coli strain XL1-blue pXL2340 (1 μg of proteins) is incubated for 1 h at 37° C. in 30 μl of 50 mM Tris/HCl buffer pH 7.7 containing 4 mM ATP, 6 mM MgCl₂, 5 mM DTT, 1 mM spermidine, 20 mM KCl, 50 μg/ml of bovine serum albumin and 500 ng of supercoiled plasmid pBR322. The reaction is stopped by adding 7 μl of a 5% SDS and 2.5 mg/ml proteinase K mixture and the samples are incubated for a second period of 30 min at 37° C. and then analysed by electrophoresis on 1% agarose gel in 0.1M Tris/borate buffer pH 8.3 containing 2 mM EDTA at 6V/cm for 3 h. The separation of the relaxed and nicked (open circular) DNAs is carried out by performing an additional 2 h electrophoretic run after addition of ethidium bromide (1 μg/ml) to the running buffer. The DNA is then quantified by scanning the negatives of photographs of the gels (Polaroid type 665 film) with the aid of a Bioimage 50S apparatus (Millipore).

[0077]FIG. 4 shows that the acellular extracts of the strains E. coli XL1-blue pXL2320 and E. coli XL1-blue pXL2340 exhibit in a mixture an intense DNA relaxing activity whereas each of the extracts is inactive when it is incubated alone. The reaction is ATP-dependent. Furthermore, these two extracts, alone or in the form of a mixture, exhibit no DNA supercoiling activity, an activity typical of gyrase.

[0078] Th ATP-dependent activity of decatenation of intertwined circular DNA molecules (catenanes) can be detected by carrying out the procedure, for example, in the following manner: a mixture of an extract of the E. coli strain XL1-blue pXL2320 (2.5 μg of proteins) and of an extract of the E. coli strain XL1-blue pXL2340 (2.5 μg of proteins) is incubated for 1 h at 37° C. in 40 μl of 50 mM Tris/HCl buffer pH 7.7 containing 1 mM ATP, 6 mM MgCl2, 200 mM glutamate, 10 mM DTT, 10 mM NaCl, 50 μg/ml of bovine serum albumin and 800 ng of kinetoplast DNA [consisting of a network of intertwined DNA molecules (catenanes) obtained from Crithidia fasciculata; TopoGene]. The reaction is stopped by adding 7 μl of a 250 mM EDTA solution (incubation 5 min at 37° C.), 5 μl of a 5% SDS and 2.5 mg/ml proteinase K mixture (incubation 30 min at 37° C.). The mixture is then analysed by electrophoresis on a 1% agarose gel in a 0.1M Tris/borate buffer pH 8.3 containing 2 mM EDTA at 6V/cm for 2 h 30 min. After staining the DNA with ethidium bromide (1 μg/ml), the DNA is quantified by scanning the negatives of photographs of the gels (Polaroid type 665 film) with the aid of a Bioimage 50S apparatus (Millipore). By working, for example, under the conditions described above, the extracts of the two strains E. coli XL1-blue pXL2320 and E. coli XL1-blue pXL2340 exhibit, in the form of a mixture, an activity of complete decatenation of the starting kinetoplast DNA. This activity is detected by the appearance of a DNA band with a size of about 2.5 kb and by the disappearance of the band of catenated DNA of very large size which penetrates very little into the gel during the electrophoretic run (FIG. 5). The E. coli gyrase introduced as a control into this assay exhibits no decatehation activity contrary to DNA topoisomerase IV of E. coli which completely decatenates the kinetoplast DNA (FIG. 5).

EXAMPLE 8 DNA Topoisomerase IV Activity of the GrlAB Protein of S. aureus whose GrlA Subunit Exhibits a Substitution of the Residue Ser-80 to Tyr (Ser-80→Tyr)

[0079] 8.1—Preparation of a Cell Extract Containing the GrlAB protein of S. aureus whose GrlA Subunit Exhibits a substitution of the residue Ser-80 to Tyr (Ser-80→Tyr).

[0080] This example illustrates how an acellular extract containing the protein GrlA_((Ser-80→Tyr))B can be prepared, and how the enzymatic activity of the protein GrlA_((Ser-80→Tyr))B can be detected and measured.

[0081] An acellular extract of the E. coli strain XL1-Blue pXL2742 expressing the protein GrlA_((Ser-80→Tyr)) is prepared, for example, as described in Example 7 for the wild-type GrlA protein.

[0082] 8.2—Purification of a DNK Topoisomerase IV of S. aureus Exhibiting an Ser-80-Tyr mutation in the GrlA Subunit.

[0083] This example illustrates how a topoisomerase IV of S. aureus exhibiting an Ser-80→Tyr mutation in the GrlA subunit can be purified. The GrlA subunit of topoisomerase IV having an Ser-80→Tyr mutation is purified according to a procedure identical to that described in Example 7.2 using a culture of the E. coli strain XL1-blue pXL2742 constructed as described in Example 6.

[0084] 8.3—Detection of the Enzymatic Activities.

[0085] The ATP-dependent activities of supercoiled DNA relaxation, on the one hand, and of decatenation of intertwined circular DNA molecules, on the other hand, are detected in this extract as described in Example 7, by incubating, in the same reaction mixture, an acellular extract of the E. coli strain XL1-Blue pXL2742 containing the protein GrlA_((Ser-80→Tyr)) and an extract of the E. coli strain XL1-Blue pXL2320 containing the GrlB protein.

EXAMPLE 9 Inhibition by Fluoroquinolones, of the DNA Topoisomerase IV Activity of the Wild-type GrlAB Protein of S. aureus and Resistance to Fluoroquinolones of the Protein Containing an Ser-80→Tyr Transition in the GrlA subunit

[0086] The two methods described in Example 7 for the assay of DNA topoisomerase IV activities can be used to detect novel molecules which act as inhibitors of topoisom rase IV of S. aureus or to characterize the behaviour of topoisomerase IV of S. aureus towards molecules already identified as inhibitors of other topoisomerases (for example the fluoroquinolones).

[0087] In the test of relaxation of supercoiled DNA for example, the disappearance or the decrease in the relaxed DNA band during analysis of the reaction mixture after incubation of the GrlAB protein of S. aureus in the presence of a molecule or of a mixture of several molecules indicates that this molecule (or these molecules), inhibit the relaxation activity of GrlAB, and is therefore potentially antibacterial. However, since the studies carried out up until now (described in Example 7) have demonstrated that the GrlAB protein is a topoisomerase IV, and since it is nowadays established that the major function of the topoisomerases IV is decatenation (or disentanglement) of the intertwined daughter chromosomes during the final stages of replication, it seems more judicious to search for the inhibitors of the GrlAB protein using a test of decatenation of DNA using, for example, the test described in Example 7.3. To carry out the experiments described in the examples which follow, the incubations are carried out with the purified wild-type GrlAB proteins as described in Example 7, and with the mutant protein GrlA_((Ser-80→Tr))B as described in Example 8. The two wild-type and mutant GrlAB proteins are reconstituted by mixing equimolar quantities of their two GrlA and GrlB subunits.

[0088] In the decatenation test, if the disappearance or the decrease in the intensity of the decatenated DNA band is observed during analysis of the reaction mixture after incubation of the GrlAB protein in the presence of a molecule or of a mixture of several molecules, this indicates that this molecule (or these molecules) inhibits the decatenation activity of the GrlAB protein, and is therefore potentially antibacterial. Since it has been demonstrated in the present invention that the GrlAB protein is the primary target for the molecules of the fluoroquinolone family, it appears that the fluoroquinolones must act as inhibitors in the decatenation test described in Example 7. Indeed, when the purified GrlAB protein is incubated in the presence of increasing quantities of a fluoroquinolone, for example ciprofloxacin, it appears that above a concentration of 10 μg/ml, ciprofloxacin completely inhibits the activity of decatenation of the kinetoplast DNA. Ciprofloxacin inhibits 50% of the activity of decatenation of kinetoplast DNA at a concentration of 4.0 μg/ml.

[0089] Likewise, sparfloxacin which is another fluoroquinolone inhibits 50% of the activity of decatenation of kinetoplast DNA at a concentration of 6.0 μg/ml. Likewise, since it has been demonstrated in the present invention (Example 4) that the presence of an Ser-80→Tyr mutation on the GrlA subunit of the mutant GrlAB protein confers on the strain a certain level of resistance to fluoroquinolones, for example ciprofloxacin, it appears that the fluoroquinolones must act on this mutant DNA topoisomeras IV as inhibitors which are less efficient in the decatenation test described in Example 7.

[0090] Indeed, when the mutant protein GrlA_((Ser-80→Tyr))B is incubated in the presence of increasing quantities of a fluoroquinolone, for example ciprofloxacin, it appears that ciprofloxacin inhibits 50% of the activity of decatenation of kinetoplast DNA at a concentration of 60 μg/ml, that is to say a concentration 15 times as high as that necessary to obtain the same effect with the wild-type enzyme.

[0091] Likewise, in the presence of the mutant enzyme GrlA_((Ser-80→Tyr))B, sparfloxacin inhibits 50% of the activity of decatenation of kinetoplast DNA at a concentration of 500 μg/ml, that is to say a concentration 80 times as high as that necessary to obtain the same effect with the wild-type enzyme.

[0092] Norfloxacin inhibits 50% of the activity of decatenation of kinetoplast DNA at a concentration of 12 μg/ml with the wild-type GrlAB enzyme and exhibits the same inhibitory activity at a concentration of 125 μg/ml with the enzyme GrlA_((Ser-80→Tyr))B. Ofloxacin inhibits 50% of the activity of decatenation of kin toplast DNA at a concentration of 10 μg/ml with the wild-typ GrlAB nzyme and has the sam inhibitory activity at a concentration of 250 μg/ml with the enzyme GrlA_((Ser-80→Tyr))B.

[0093] Novobiocin, whos mechanism of action is different from that of the fluoroquinolones, should therefor in principle have the same inhibitory activity on both the wild-type GrlAB enzyme and on the mutant GrlA_((Ser-80→Tyr))B enzyme in the decatenation test described in Example 7. Indeed, novobiocin inhibits 50%, of the activity of decatenation of kinetoplast DNA at a concentration of about 30 μg/ml whatever the enzyme used (wild-type GrlAB or mutant GrlA_((Ser-80→Tyr))).

ABBREVIATIONS

[0094] DNA: deoxyribonucleic acid

[0095] RNA: ribonucleic acid

[0096] MIC: minimum inhibitory concentration

[0097] IPTG: isopropylthio-β-D-galactoside

[0098] LB: Luria-Bertani medium

[0099] PAGE: electrophoresis gel containing acrylamide and N,N′-methylenebisacrylamide

[0100] PCR: polymerase chain reaction

[0101] pfu: plaque forming unit

[0102] QRDR: region of the GyrA subunit where the point mutations leading to resistance to fluoroquinolones are mapped

[0103] SDS: sodium dodecyl sulphate

[0104] Tris: tris(hydroxymethyl)aminomethane

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1 17 4565 base pairs nucleic acid single linear cDNA 1 GAATTCCGAC GTACGTTTGC AGGAGGCGAA ATCATTGGCA ATGAATAAAC AAAATAATTA 60 TTCAGATGAT TCAATACAGG TTTTAGAGGG GTTAGAAGCA GTTCGTAAAA GACCTGGTAT 120 GTATATTGGA TCAACTGATA AACGGGGATT ACATCATCTA GTATATGAAA TTGTCGATAA 180 CTCCGTCGAT GAAGTATTGA ATGGTTACGG TAACGAAATA GATGTAACAA TTAATAAAGA 240 TGGTAGTATT TCTATAGAAG ATAATGGACG TGGTATGCCA ACAGGTATAC ATAAATCAGG 300 TAAACCGACA GTCGAAGTTA TCTTTACTGT TTTACATGCA GGAGGTAAAT TTGGACAAGG 360 TGGCTATAAA ACTTCAGGTG GTCTTCACGG CGTTGGTGCT TCAGTGGTAA ATGCATTGAG 420 TGAATGGCTT GAAGTTGAAA TCCATCGAGA TGGTAATATA TATCATCAAA GTTTTAAAAA 480 CGGTGGTTCG CCATCTTCAG GTTTAGTGAA AAAAGGTAAA ACTAAGAAAA CAGGTACCAA 540 AGTAACATTT AAACCTGATG ACACAATTTT TAAAGCATCT ACATCATTTA ATTTTGATGT 600 TTTAAGTGAA CGACTACAAG AGTCTGCGTT CTTATTGAAA AATTTAAAAA TAACGCTTAA 660 TGATTTACGC AGTGGTAAAG AGCGTCAAGA GCATTACCAT TATGAAGAAG GAATCAAAGA 720 GTTTGTTAGT TATGTCAATG AAGGAAAAGA AGTTTTGCAT GACGTGGCTA CATTTTCAGG 780 TGAAGCAAAT GGTATAGAGG TAGACGTAGC TTTCCAATAT AATGATCAAT ATTCAGAAAG 840 TATTTTAAGT TTTGTAAATA ATGTACGTAC TAAAGATGGT GGTACACATG AAGTTGGTTT 900 TAAAACAGCA ATGACACGCG TATTTAATGA TTATGCACGT CGTATTAATG AACTTAAAAC 960 AAAAGATAAA AACTTAGATG GTAATGATAT TCGTGAAGGT TTAACAGCTG TTGTGTCTGT 1020 TCGTATTCCA GAAGAATTAT TGCAATTTGA AGGACAAACG AAATCTAAAT TGGGTACTTC 1080 TGAAGCTAGA AGTGCTGTTG ATTCAGTTGT TGCAGACAAA TTGCCATTCT ATTTAGAAGA 1140 AAAAGGACAA TTGTCTAAAT CACTTGTGAA AAAAGCGATT AAAGCACAAC AAGCAAGGGA 1200 AGCTGCACGT AAAGCTCGTG AAGATGCTCG TTCAGGTAAG AAAAACAAGC GTAAAGACAC 1260 TTTGCTATCT GGTAAATTAA CACCTGCACA AAGTAAAAAC ACTGAAAAAA ATGAATTGTA 1320 TTTAGTCGAA GGTGATTCTG CGGGAGGTTC AGCAAAACTT GGACGAGACC GCAAATTCCA 1380 AGCGATATTA CCATTACGTG GTAAGGTAAT TAATACAGAG AAAGCACGTC TAGAAGATAT 1440 TTTTAAAAAT GAAGAAATTA ATACAATTAT CCACACAATC GGGGCAGGCG TTGGTACTGA 1500 CTTTAAAATT GAAGATAGTA ATTATAATCG TGTAATTATT ATGACTGATG CTGATACTGA 1560 TGGTGCGCAT ATTCAAGTGC TATTGTTAAC ATTCTTCTTC AAATATATGA AACCGCTTGT 1620 TCAAGCAGGT CGTGTATTTA TTGCTTTACC TCCACTTTAT AAATTGGAAA AAGGTAAAGG 1680 CAAAACAAAG CGAGTTGAAT ACGCTTGGAC AGACGAAGAG CTTAATAAAT TGCAAAAAGA 1740 ACTTGGTAAA GGCTTCACGT TACAACGTTA CAAAGGTTTG GGTGAAATGA ACCCTGAACA 1800 ATTATGGGAA ACGACGATGA ACCCAGAAAC ACGAACTTTA ATTCGTGTAC AAGTTGAAGA 1860 TGAAGTGCGT TCATCTAAAC GTGTAACAAC ATTAATGGGT GACAAAGTAC AACCTAGACG 1920 TGAATGGATT GAAAAGCATG TTGAGTTTGG TATGCAAGAG GACCAAAGTA TTTTAGATAA 1980 TTCTGAAGTA CAAGTGCTTG AAAATGATCA ATTTGATGAG GAGGAAATCT AGTGAGTGAA 2040 ATAATTCAAG ATTTATCACT TGAAGATGTT TTAGGTGATC GCTTTGGAAG ATATAGTAAA 2100 TATATTATTC AAGAGCGTGC ATTGCCAGAT GTTCGTGATG GTTTAAAACC AGTACAACGT 2160 CGTATTTTAT ACGCAATGTA TTCAAGTGGT AATACACACG ATAAAAATTT CCGTAAAAGT 2220 GCGAAAACAG TCGGTGATGT TATTGGTCAA TATCATCCAC ATGGAGACTC CTCAGTGTAC 2280 GAAGCAATGG TCCGTTTAAG TCAAGACTGG AAGTTACGAC ATGTCTTAAT AGAAATGCAT 2340 GGTAATAATG GTAGTATCGA TAATGATCCG CCAGCGGCAA TGCGTTACAC TGAAGCTAAG 2400 TTAAGCTTAC TAGCTGAAGA GTTATTACGT GATATTAATA AAGAGACAGT TTCTTTCATT 2460 CCAAACTATG ATGATACGAC ACTCGAACCA ATGGTATTGC CATCAAGATT TCCTAACTTA 2520 CTAGTGAATG GTTCTACAGG TATATCTGCA GGTTACGCGA CAGATATACC ACCACATAAT 2580 TTAGCTGAAG TGATTCAAGC AACACTTAAA TATATTGATA ATCCGGATAT TACAGTCAAT 2640 CAATTAATGA AATATATTAA AGGTCCTGAT TTTCCAACTG GTGGTATTAT TCAAGGTATT 2700 GATGGTATTA AAAAAGCTTA TGAATCAGGT AAAGGTAGAA TTATAGTTCG TTCTAAAGTT 2760 GAAGAAGAAA CTTTACGCAA TGGACGTAAA CAGTTAATTA TTACTGAAAT TCCATATGAA 2820 GTGAACAAAG GTAGCTTAGT AAAACGTATC GATGAATTAC GTGCTGACAA AAAAGTCGAT 2880 GGTATCGTTG AAGTACGTGA TGAAACTGAT AGAACTGGTT TACGAATAGC AATTGAATTG 2940 AAAAAAGATG TGAACAGTGA ATCAATCAAA AATTATCTTT ATAAAAACTC TGATTTACAG 3000 ATTTCATATA ATTTCAACAT GGTCGCTATT AGTGATGGTC GTCCAAAATT GATGGGTATT 3060 CGTCAAATTA TAGATAGTTA TTTGAATCAT CAAATTGAGG TTGTTGCAAA TAGAACGAAG 3120 TTTGAATTAG ATAATGCTGA AAAACGTATG CATATCGTTG AAGGTTTGAT TAAAGCGTTG 3180 TCAATTTTAG ATAAAGTAAT CGAATTGATT CGTAGCTCTA AAAACAAGCG TGACGCTAAA 3240 GAAAACCTTA TCGAAGTATA CGAGTTCACA GAAGAACAGG CTGAAGCAAT TGTAATGTTA 3300 CAGTTATATC GTTTAACAAA CACTGACATA GTTGCGCTTG AAGGTGAACA TAAAGAACTT 3360 GAAGCATTAA TCAAACAATT ACGTCATATT CTTGATAACC ATGATGCATT ATTGAATGTC 3420 ATAAAAGAAG AATTGAATGA AATTAAAAAG AAATTCAAAT CTGAACGACT GTCTTTAATT 3480 GAAGCAGAAA TTGAAGAAAT TAAAATTGAC AAAGAAGTTA TGGTGCCTAG TGAAGAAGTT 3540 ATTTTAAGTA TGACACGTCA TGGATATATT AAACGTACTT CTATTCGTAG CTTTAATGCT 3600 AGCGGTGTTG AAGATATTGG TTTAAAAGAT GGTGACAGTT TACTTAAACA TCAAGAAGTA 3660 AATACGCAAG ATACCGTACT AGTATTTACA AATAAAGGTC GTTATCTATT TATACCAGTT 3720 CATAAATTAC GAGATATTCG TTGGAAAGAA TTGGGGCAAC ATGTATCACA AATAGTTCCT 3780 ATCGAAGAAG ATGAAGTGGT TATTAATGTC TATAATGAAA AGGACTTTAA TACTGATGCA 3840 TTTTATGTTT TTGCGACTCA AAATGGCATG ATTAAGAAAA GTACAGTGCC TCTATTTAAA 3900 ACAACGCGTT TTAATAAACC TTTAATTGCA ACTAAAGTTA AAGAAAATGA TGATTTGATT 3960 AGTGTTATGC GCTTTGAAAA AGATCAATTA ATTACCGTAA TTACAAATAA AGGTATGTCA 4020 TTAACGTATA ATACAAGTGA ACTATCAGAT ACTGGATTAA GGGCGGCTGG TGTTAAATCA 4080 ATAAATCTTA AAGTTGAAGA TTTCGTTGTT ATGACAGAAG GTGTTTCTGA AAATGATACT 4140 ATATTGATGG CCACACAACG CGGCTCGTTA AAACGTATTA GTTTTAAAAT CTTACAAGTT 4200 GCTAAAAGAG CACAACGTGG AATAACTTTA TTAAAAGAAT TAAAGAAAAA TCCACATCGT 4260 ATAGTAGCTG CACATGTAGT GACAGGTGAA CATAGTCAAT ATACATTATA TTCAAAATCA 4320 AACGAAGAAC ATGGTTTAAT TAATGATATT CATAAATCTG AACAATATAC AAATGGCTCA 4380 TTCATTGTAG ATACAGATGA TTTTGGTGAA GTAATAGACA TGTATATTAG CTAAAAACTA 4440 TATGCAATCA CGAAATTAAA TGATAAAATA CAGTAATGTT AAATTTTGAC TAAATTCAAG 4500 GGATTTATAT TAAATGCTGA CCAAGTACTT ATCGTTAAAT TAGCGATACG GAATCCGCGG 4560 AATTC 4565 4565 base pairs nucleic acid single linear cDNA 2 CTTAAGGCTG CATGCAAACG TCCTCCGCTT TAGTAACCGT TACTTATTTG TTTTATTAAT 60 AAGTCTACTA AGTTATGTCC AAAATCTCCC CAATCTTCGT CAAGCATTTT CTGGACCATA 120 CATATAACCT AGTTGACTAT TTGCCCCTAA TGTAGTAGAT CATATACTTT AACAGCTATT 180 GAGGCAGCTA CTTCATAACT TACCAATGCC ATTGCTTTAT CTACATTGTT AATTATTTCT 240 ACCATCATAA AGATATCTTC TATTACCTGC ACCATACGGT TGTCCATATG TATTTAGTCC 300 ATTTGGCTGT CAGCTTCAAT AGAAATGACA AAATGTACGT CCTCCATTTA AACCTGTTCC 360 ACCGATATTT TGAAGTCCAC CAGAAGTGCC GCAACCACGA AGTCACCATT TACGTAACTC 420 ACTTACCGAA CTTCAACTTT AGGTAGCTCT ACCATTATAT ATAGTAGTTT CAAAATTTTT 480 GCCACCAAGC GGTAGAAGTC CAAATCACTT TTTTCCATTT TGATTCTTTT GTCCATGGTT 540 TCATTGTAAA TTTGGACTAC TGTGTTAAAA ATTTCGTAGA TGTAGTAAAT TAAAACTACA 600 AAATTCACTT GCTGATGTTC TCAGACGCAA GAATAACTTT TTAAATTTTT ATTGCGAATT 660 ACTAAATGCG TCACCATTTC TCGCAGTTCT CGTAATGGTA ATACTTCTTC CTTAGTTTCT 720 CAAACAATCA ATACAGTTAC TTCCTTTTCT TCAAAACGTA CTGCACCGAT GTAAAAGTCC 780 ACTTCGTTTA CCATATCTCC ATCTGCATCG AAAGGTTATA TTACTAGTTA TAAGTCTTTC 840 ATAAAATTCA AAACATTTAT TACATGCATG ATTTCTACCA CCATGTGTAC TTCAACCAAA 900 ATTTTGTCGT TACTGTGCGC ATAAATTACT AATACGTGCA GCATAATTAC TTGAATTTTG 960 TTTTCTATTT TTGAATCTAC CATTACTATA AGCACTTCCA AATTGTCGAC AACACAGACA 1020 AGCATAAGGT CTTCTTAATA ACGTTAAACT TCCTGTTTGC TTTAGATTTA ACCCATGAAG 1080 ACTTCGATCT TCACGACAAC TAAGTCAACA ACGTCTGTTT AACGGTAAGA TAAATCTTCT 1140 TTTTCCTGTT AACAGATTTA GTGAACACTT TTTTCGCTAA TTTCGTGTTG TTCGTTCCCT 1200 TCGACGTGCA TTTCGAGCAC TTCTACGAGC AAGTCCATTC TTTTTGTTCG CATTTCTGTG 1260 AAACGATAGA CCATTTAATT GTGGACGTGT TTCATTTTTG TGACTTTTTT TACTTAACAT 1320 AAATCAGCTT CCACTAAGAC GCCCTCCAAG TCGTTTTGAA CCTGCTCTGG CGTTTAAGGT 1380 TCGCTATAAT GGTAATGCAC CATTCCATTA ATTATGTCTC TTTCGTGCAG ATCTTCTATA 1440 AAAATTTTTA CTTCTTTAAT TATGTTAATA GGTGTGTTAG CCCCGTCCGC AACCATGACT 1500 GAAATTTTAA CTTCTATCAT TAATATTAGC ACATTAATAA TACTGACTAC GACTATGACT 1560 ACCACGCGTA TAAGTTCACG ATAACAATTG TAAGAAGAAG TTTATATACT TTGGCGAACA 1620 AGTTCGTCCA GCACATAAAT AACGAAATGG AGGTGAAATA TTTAACCTTT TTCCATTTCC 1680 GTTTTGTTTC GCTCAACTTA TGCGAACCTG TCTGCTTCTC GAATTATTTA ACGTTTTTCT 1740 TGAACCATTT CCGAAGTGCA ATGTTGCAAT GTTTCCAAAC CCACTTTACT TGGGACTTGT 1800 TAATACCCTT TGCTGCTACT TGGGTCTTTG TGCTTGAAAT TAAGCACATG TTCAACTTCT 1860 ACTTCACGCA AGTAGATTTG CACATTGTTG TAATTACCCA CTGTTTCATG TTGGATCTGC 1920 ACTTACCTAA CTTTTCGTAC AACTCAAACC ATACGTTCTC CTGGTTTCAT AAAATCTATT 1980 AAGACTTCAT GTTCACGAAC TTTTACTAGT TAAACTACTC CTCCTTTAGA TCACTCACTT 2040 TATTAAGTTC TAAATAGTGA ACTTCTACAA AATCCACTAG CGAAACCTTC TATATCATTT 2100 ATATAATAAG TTCTCGCACG TAACGGTCTA CAAGCACTAC CAAATTTTGG TCATGTTGCA 2160 GCATAAAATA TGCGTTACAT AAGTTCACCA TTATGTGTGC TATTTTTAAA GGCATTTTCA 2220 CGCTTTTGTC AGCCACTACA ATAACCAGTT ATAGTAGGTG TACCTCTGAG GAGTCACATG 2280 CTTCGTTACC AGGCAAATTC AGTTCTGACC TTCAATGCTG TACAGAATTA TCTTTACGTA 2340 CCATTATTAC CATCATAGCT ATTACTAGGC GGTCGCCGTT ACGCAATGTG ACTTCGATTC 2400 AATTCGAATG ATCGACTTCT CAATAATGCA CTATAATTAT TTCTCTGTCA AAGAAAGTAA 2460 GGTTTGATAC TACTATGCTG TGAGCTTGGT TACCATAACG GTAGTTCTAA AGGATTGAAT 2520 GATCACTTAC CAAGATGTCC ATATAGACGT CCAATGCGCT GTCTATATGG TGGTGTATTA 2580 AATCGACTTC ACTAAGTTCG TTGTGAATTT ATATAACTAT TAGGCATATA ATGTCAGTTA 2640 GTTAATTACT TTATATAATT TCCAGGACTA AAAGGTTGAC CACCATAATA AGTTCCATAA 2700 CTACCATAAT TTTTTCGAAT ACTTAGTCCA TTTCCATCTT AATATCAAGC AAGATTTCAA 2760 CTTCTTCTTT GAAATGCGTT ACCTGCATTT GTCAATTAAT AATGACTTTA AGGTATACTT 2820 CACTTGTTTC CATCGAATCA TTTTGCATAG CTACTTAATG CACGACTGTT TTTTCAGCTA 2880 CCATAGCAAC TTCATGCACT ACTTTGACTA TCTTGACCAA ATGCTTATCG TTAACTTAAC 2940 TTTTTTCTAC ACTTGTCACT TAGTTAGTTT TTAATAGAAA TATTTTTGAG ACTAAATGTC 3000 TAAAGTATAT TAAAGTTGTA CCAGCGATAA TCACTACCAG CAGGTTTTAA CTACCCATAA 3060 GCAGTTTAAT ATCTATCAAT AAACTTAGTA GTTTAACTCC AACAACGTTT ATCTTGCTTC 3120 AAACTTAATC TATTACGACT TTTTGCATAC GTATAGCAAC TTCCAAACTA ATTTCGCAAC 3180 AGTTAAAATC TATTTCATTA GCTTAACTAA GCATCGAGAT TTTTGTTCGC ACTGCGATTT 3240 CTTTTGGAAT AGCTTCATAT GCTCAAGTGT CTTCTTGTCC GACTTCGTTA ACATTACAAT 3300 GTCAATATAG CAAATTGTTT GTGACTGTAT CAACGCGAAC TTCCACTTGT ATTTCTTGAA 3360 CTTCGTAATT AGTTTGTTAA TGCAGTATAA GAACTATTGG TACTACGTAA TAACTTACAG 3420 TATTTTCTTC TTAACTTACT TTAATTTTTC TTTAAGTTTA GACTTGCTGA CAGAAATTAA 3480 CTTCGTCTTT AACTTCTTTA ATTTTAACTG TTTCTTCAAT ACCACGGATC ACTTCTTCAA 3540 TAAAATTCAT ACTGTGCAGT ACCTATATAA TTTGCATGAA GATAAGCATC GAAATTACGA 3600 TCGCCACAAC TTCTATAACC AAATTTTCTA CCACTGTCAA ATGAATTTGT AGTTCTTCAT 3660 TTATGCGTTC TATGGCATGA TCATAAATGT TTATTTCCAG CAATAGATAA ATATGGTCAA 3720 GTATTTAATG CTCTATAAGC AACCTTTCTT AACCCCGTTG TACATAGTGT TTATCAAGGA 3780 TAGCTTCTTC TACTTCACCA ATAATTACAG ATATTACTTT TCCTGAAATT ATGACTACGT 3840 AAAATACAAA AACGCTGAGT TTTACCGTAC TAATTCTTTT CATGTCACGG AGATAAATTT 3900 TGTTGCGCAA AATTATTTGG AAATTAACGT TGATTTCAAT TTCTTTTACT ACTAAACTAA 3960 TCACAATACG CGAAACTTTT TCTAGTTAAT TAATGGCATT AATGTTTATT TCCATACAGT 4020 AATTGCATAT TATGTTCACT TGATAGTCTA TGACCTAATT CCCGCCGACC ACAATTTAGT 4080 TATTTAGAAT TTCAACTTCT AAAGCAACAA TACTGTCTTC CACAAAGACT TTTACTATGA 4140 TATAACTACC GGTGTGTTGC GCCGAGCAAT TTTGCATAAT CAAAATTTTA GAATGTTCAA 4200 CGATTTTCTC GTGTTGCACC TTATTGAAAT AATTTTCTTA ATTTCTTTTT AGGTGTAGCA 4260 TATCATCGAC GTGTACATCA CTGTCCACTT GTATCAGTTA TATGTAATAT AAGTTTTAGT 4320 TTGCTTCTTG TACCAAATTA ATTACTATAA GTATTTAGAC TTGTTATATG TTTACCGAGT 4380 AAGTAACATC TATGTCTACT AAAACCACTT CATTATCTGT ACATATAATC GATTTTTGAT 4440 ATACGTTAGT GCTTTAATTT ACTATTTTAT GTCATTACAA TTTAAAACTG ATTTAAGTTC 4500 CCTAAATATA ATTTACGACT GGTTCATGAA TAGCAATTTA ATCGCTATGC CTTAGGCGCC 4560 TTAAG 4565 800 amino acids amino acid single linear peptide 3 Met Ser Glu Ile Ile Gln Asp Leu Ser Leu Glu Asp Val Leu Gly Asp 1 5 10 15 Arg Phe Gly Arg Tyr Ser Lys Tyr Ile Ile Gln Glu Arg Ala Leu Pro 20 25 30 Asp Val Arg Asp Gly Leu Lys Pro Val Gln Arg Arg Ile Leu Tyr Ala 35 40 45 Met Tyr Ser Ser Gly Asn Thr His Asp Lys Asn Phe Arg Lys Ser Ala 50 55 60 Lys Thr Val Gly Asp Val Ile Gly Gln Tyr His Pro His Gly Asp Ser 65 70 75 80 Ser Val Tyr Glu Ala Met Val Arg Leu Ser Gln Asp Trp Lys Leu Arg 85 90 95 His Val Leu Ile Glu Met His Gly Asn Asn Gly Ser Ile Asp Asn Asp 100 105 110 Pro Pro Ala Ala Met Arg Tyr Thr Glu Ala Lys Leu Ser Leu Leu Ala 115 120 125 Glu Glu Leu Leu Arg Asp Ile Asn Lys Glu Thr Val Ser Phe Ile Pro 130 135 140 Asn Tyr Asp Asp Thr Thr Leu Glu Pro Met Val Leu Pro Ser Arg Phe 145 150 155 160 Pro Asn Leu Leu Val Asn Gly Ser Thr Gly Ile Ser Ala Gly Tyr Ala 165 170 175 Thr Asp Ile Pro Pro His Asn Leu Ala Glu Val Ile Gln Ala Thr Leu 180 185 190 Lys Tyr Ile Asp Asn Pro Asp Ile Thr Val Asn Gln Leu Met Lys Tyr 195 200 205 Ile Lys Gly Pro Asp Phe Pro Thr Gly Gly Ile Ile Gln Gly Ile Asp 210 215 220 Gly Ile Lys Lys Ala Tyr Glu Ser Gly Lys Gly Arg Ile Ile Val Arg 225 230 235 240 Ser Lys Val Glu Glu Glu Thr Leu Arg Asn Gly Arg Lys Gln Leu Ile 245 250 255 Ile Thr Glu Ile Pro Tyr Glu Val Asn Lys Gly Ser Leu Val Lys Arg 260 265 270 Ile Asp Glu Leu Arg Ala Asp Lys Lys Val Asp Gly Ile Val Glu Val 275 280 285 Arg Asp Glu Thr Asp Arg Thr Gly Leu Arg Ile Ala Ile Glu Leu Lys 290 295 300 Lys Asp Val Asn Ser Glu Ser Ile Lys Asn Tyr Leu Tyr Lys Asn Ser 305 310 315 320 Asp Leu Gln Ile Ser Tyr Asn Phe Asn Met Val Ala Ile Ser Asp Gly 325 330 335 Arg Pro Lys Leu Met Gly Ile Arg Gln Ile Ile Asp Ser Tyr Leu Asn 340 345 350 His Gln Ile Glu Val Val Ala Asn Arg Thr Lys Phe Glu Leu Asp Asn 355 360 365 Ala Glu Lys Arg Met His Ile Val Glu Gly Leu Ile Lys Ala Leu Ser 370 375 380 Ile Leu Asp Lys Val Ile Glu Leu Ile Arg Ser Ser Lys Asn Lys Arg 385 390 395 400 Asp Ala Lys Glu Asn Leu Ile Glu Val Tyr Glu Phe Thr Glu Glu Gln 405 410 415 Ala Glu Ala Ile Val Met Leu Gln Leu Tyr Arg Leu Thr Asn Thr Asp 420 425 430 Ile Val Ala Leu Glu Gly Glu His Lys Glu Leu Glu Ala Leu Ile Lys 435 440 445 Gln Leu Arg His Ile Leu Asp Asn His Asp Ala Leu Leu Asn Val Ile 450 455 460 Lys Glu Glu Leu Asn Glu Ile Lys Lys Lys Phe Lys Ser Glu Arg Leu 465 470 475 480 Ser Leu Ile Glu Ala Glu Ile Glu Glu Ile Lys Ile Asp Lys Glu Val 485 490 495 Met Val Pro Ser Glu Glu Val Ile Leu Ser Met Thr Arg His Gly Tyr 500 505 510 Ile Lys Arg Thr Ser Ile Arg Ser Phe Asn Ala Ser Gly Val Glu Asp 515 520 525 Ile Gly Leu Lys Asp Gly Asp Ser Leu Leu Lys His Gln Glu Val Asn 530 535 540 Thr Gln Asp Thr Val Leu Val Phe Thr Asn Lys Gly Arg Tyr Leu Phe 545 550 555 560 Ile Pro Val His Lys Leu Arg Asp Ile Arg Trp Lys Glu Leu Gly Gln 565 570 575 His Val Ser Gln Ile Val Pro Ile Glu Glu Asp Glu Val Val Ile Asn 580 585 590 Val Tyr Asn Glu Lys Asp Phe Asn Thr Asp Ala Phe Tyr Val Phe Ala 595 600 605 Thr Gln Asn Gly Met Ile Lys Lys Ser Thr Val Pro Leu Phe Lys Thr 610 615 620 Thr Arg Pro Asn Lys Pro Leu Ile Ala Thr Lys Val Lys Glu Asn Asp 625 630 635 640 Asp Leu Ile Ser Val Met Arg Phe Glu Lys Asp Gln Leu Ile Thr Val 645 650 655 Ile Thr Asn Lys Gly Met Ser Leu Thr Tyr Asn Thr Ser Glu Leu Ser 660 665 670 Asp Thr Gly Leu Arg Ala Ala Gly Val Lys Ser Ile Asn Leu Lys Val 675 680 685 Glu Asp Phe Val Val Met Thr Glu Gly Val Ser Glu Asn Asp Thr Ile 690 695 700 Leu Met Ala Thr Gln Arg Gly Ser Leu Lys Arg Ile Ser Phe Lys Ile 705 710 715 720 Leu Gln Val Ala Lys Arg Ala Gln Arg Gly Ile Thr Leu Leu Lys Glu 725 730 735 Leu Lys Lys Asn Pro His Arg Ile Val Ala Ala His Val Val Thr Gly 740 745 750 Glu His Ser Gln Tyr Thr Leu Tyr Ser Lys Ser Asn Glu Glu His Gly 755 760 765 Leu Ile Asn Asp Ile His Lys Ser Glu Gln Tyr Thr Asn Gly Ser Phe 770 775 780 Ile Val Asp Thr Asp Asp Phe Gly Glu Val Ile Asp Met Tyr Ile Ser 785 790 795 800 2402 base pairs nucleic acid single linear cDNA 4 GTGAGTGAAA TAATTCAAGA TTTATCACTT GAAGATGTTT TAGGTGATCG CTTTGGAAGA 60 TATAGTAAAT ATATTATTCA AGAGCGTGCA TTGCCAGATG TTCGTGATGG TTTAAAACCA 120 GTACAACGTC GTATTTTATA CGCAATGTAT TCAAGTGGTA ATACACACGA TAAAAATTTC 180 CGTAAAAGTG CGAAAACAGT CGGTGATGTT ATTGGTCAAT ATCATCCACA TGGAGACTCC 240 TCAGTGTACG AAGCAATGGT CCGTTTAAGT CAAGACTGGA AGTTACGACA TGTCTTAATA 300 GAAATGCATG GTAATAATGG TAGTATCGAT AATGATCCGC CAGCGGCAAT GCGTTACACT 360 GAAGCTAAGT TAAGCTTACT AGCTGAAGAG TTATTACGTG ATATTAATAA AGAGACAGTT 420 TCTTTCATTC CAAACTATGA TGATACGACA CTCGAACCAA TGGTATTGCC ATCAAGATTT 480 CCTAACTTAC TAGTGAATGG TTCTACAGGT ATATCTGCAG GTTACGCGAC AGATATACCA 540 CCACTAATTT AGCTGAAGTG ATTCAAGCAA CACTTAAATA TATTGATAAT CCGGATATTA 600 TAGTCAATCA ATTAATGAAA TATATTAAAG GTCCTGATTT TCCAACTGGT GGTATTATTC 660 AAGGTATTGA TGGTATTAAA AAAGCTTATG AATCAGGTAA AGGTAGAATT ATAGTTCGTT 720 CTAAAGTTGA AGAAGAAATT TTACGCAATG GACGTAAACA GTTAATTATT ACTGAAATTC 780 CATATGAAGT GAACAAAGGT AGCTTAGTAA AACGTATCGA TGAATTACGT GCTGACAAAA 840 AAGTCGATGG TATCGTTGAA GTACGTGATG AAACTGATAG AACTGGTTTA CGAATAGCAA 900 TTGAATTGAA AAAAGATGTG AACAGTGAAT CAATCAAAAA TTATCTTTAT AAAAACTCTG 960 ATTTACAGAT TTCATATAAT TTCAACATGG TCGCTATTAG TGATGGTCGT CCAAAATTGA 1020 TGGGTATTCG TCAAATTATA GATAGTTATT TGAATCATCA AATTGAGGTT GTTGCAAATA 1080 GAACGAAGTT TGAATTAGAT AATGCTGAAA AACGTATGCA TATCGTTGAA GGTTTGATTA 1140 AAGCGTTGTC AATTTTAGAT AAAGTAATCG AATTGATTCG TAGCTCTAAA AACAAGCGTG 1200 ACGCTAAAGA AAACCTTATC GAAGTATACG AGTTCACAGA AGAACAGGCT GAAGCAATTG 1260 TAATGTTACA GTTATATCGT TTAACAAACA CTGACATAGT TGCGCTTGAA GGTGAACATA 1320 AAGAACTTGA AGCATTAATC AAACAATTAC GTCATATTCT TGATAACCAT GATGCATTAT 1380 TGAATGTCAT AAAAGAAGAA TTGAATGAAA TTAAAAAGAA ATTCAAATCT GAACGACTGT 1440 CTTTAATTGA AGCAGAAATT GAAGAAATTA AAATTGACAA AGAAGTTATG GTGCCTAGTG 1500 AAGAAGTTAT TTTAAGTATG ACACGTCATG GATATATTAA ACGTACTTCT ATTCGTAGCT 1560 TTAATGCTAG CGGTGTTGAA GATATTGGTT TAAAAGATGG TGACAGTTTA CTTAAACATC 1620 AAGAAGTAAA TACGCAAGAT ACCGTACTAG TATTTACAAA TAAAGGTCGT TATCTATTTA 1680 TACCAGTTCA TAAATTACGA GATATTCGTT GGAAAGAATT GGGGCAACAT GTATCACAAA 1740 TAGTTCCTAT CGAAGAAGAT GAAGTGGTTA TTAATGTTTA TAATGAAAAG GACTTTAATA 1800 CTGATGCATT TTATGTTTTT GCGACTCAAA ATGGCATGAT TAAGAAAAGT ATAGTGCCTC 1860 TATTTAAAAC AACGCGTTTT AATAAACCTT TAATTGCAAC TAAAGTTAAA GAAAATGATG 1920 ATTTGATTAG TGTTATGCGT TTTGAAAAAG ATCAATTAAT TACCGTAATT ACAAATAAAG 1980 GTATGTCATT AACGTATAAT ACAAGTGAAC TATCAGATAC TGGATTAAGG GCGGCTGGTG 2040 TTAAATCAAT AAATCTTAAA GTTGAAGATT TCGTTGTTAT GACAGAAGGT GTTTCTGAAA 2100 ATGATACTAT ATTGATGGCC ACACAACGCG GCTCGTTAAA ACGTATTAGT TTTAAAATCT 2160 TACAAGTTGC TAAAAGAGCA CAACGTGGAA TAACTTTATT AAAAGAATTA AAGAAAAATC 2220 CACATCGTAT AGTAGCTGCA CATGTAGTGA CAGGTGAACA TAGTCAATAT ACATTATATT 2280 CAAAATCAAA CGAAGAACAT GGTTTAATTA ATGATATTCA TAAATCTGAA CAATATACAA 2340 ATGGCTCATT CATTGTAGAT ACAGATGATT TTGGTGAAGT AATAGACATG TATATTAGCT 2400 AA 2402 663 amino acids amino acid single linear peptide 5 Met Asn Lys Gln Asn Asn Tyr Ser Asp Asp Ser Ile Gln Val Leu Glu 1 5 10 15 Gly Leu Glu Ala Val Arg Lys Arg Pro Gly Met Tyr Ile Gly Ser Thr 20 25 30 Asp Lys Arg Gly Leu His His Leu Val Tyr Glu Ile Val Asp Asn Ser 35 40 45 Val Asp Glu Val Leu Asn Gly Tyr Gly Asn Glu Ile Asp Val Thr Ile 50 55 60 Asn Lys Asp Gly Ser Ile Ser Ile Glu Asp Asn Gly Arg Gly Met Pro 65 70 75 80 Thr Gly Ile His Lys Ser Gly Lys Pro Thr Val Glu Val Ile Phe Thr 85 90 95 Val Leu His Ala Gly Gly Lys Phe Gly Gln Gly Gly Tyr Lys Thr Ser 100 105 110 Gly Gly Leu His Gly Val Gly Ala Ser Val Val Asn Ala Leu Ser Glu 115 120 125 Trp Leu Glu Val Glu Ile His Arg Asp Gly Asn Ile Tyr His Gln Ser 130 135 140 Phe Lys Asn Gly Gly Ser Pro Ser Ser Gly Leu Val Lys Lys Gly Lys 145 150 155 160 Thr Lys Lys Thr Gly Thr Lys Val Thr Phe Lys Pro Asp Asp Thr Ile 165 170 175 Phe Lys Ala Ser Thr Ser Phe Asn Phe Asp Val Leu Ser Glu Arg Leu 180 185 190 Gln Glu Ser Ala Phe Leu Leu Lys Asn Leu Lys Ile Thr Leu Asn Asp 195 200 205 Leu Arg Ser Gly Lys Glu Arg Gln Glu His Tyr His Tyr Glu Glu Gly 210 215 220 Ile Lys Glu Phe Val Ser Tyr Val Asn Glu Gly Lys Glu Val Leu His 225 230 235 240 Asp Val Ala Thr Phe Ser Gly Glu Ala Asn Gly Ile Glu Val Asp Val 245 250 255 Ala Phe Gln Tyr Asn Asp Gln Tyr Ser Glu Ser Ile Leu Ser Phe Val 260 265 270 Asn Asn Val Arg Thr Lys Asp Gly Gly Thr His Glu Val Gly Phe Lys 275 280 285 Thr Ala Met Thr Arg Val Phe Asn Asp Tyr Ala Arg Arg Ile Asn Glu 290 295 300 Leu Lys Thr Lys Asp Lys Asn Leu Asp Gly Asn Asp Ile Arg Glu Gly 305 310 315 320 Leu Thr Ala Val Val Ser Val Arg Ile Pro Glu Glu Leu Leu Gln Phe 325 330 335 Glu Gly Gln Thr Lys Ser Lys Leu Gly Thr Ser Glu Ala Arg Ser Ala 340 345 350 Val Asp Ser Val Val Ala Asp Lys Leu Pro Phe Tyr Leu Glu Glu Lys 355 360 365 Gly Gln Leu Ser Lys Ser Leu Val Lys Lys Ala Ile Lys Ala Gln Gln 370 375 380 Ala Arg Glu Ala Ala Arg Lys Ala Arg Glu Asp Ala Arg Ser Gly Lys 385 390 395 400 Lys Asn Lys Arg Lys Asp Thr Leu Leu Ser Gly Lys Leu Thr Pro Ala 405 410 415 Gln Ser Lys Asn Thr Glu Lys Asn Glu Leu Tyr Leu Val Glu Gly Asp 420 425 430 Ser Ala Gly Gly Ser Ala Lys Leu Gly Arg Asp Arg Lys Phe Gln Ala 435 440 445 Ile Leu Pro Leu Arg Gly Lys Val Ile Asn Thr Glu Lys Ala Arg Leu 450 455 460 Glu Asp Ile Phe Lys Asn Glu Glu Ile Asn Thr Ile Ile His Thr Ile 465 470 475 480 Gly Ala Gly Val Gly Thr Asp Phe Lys Ile Glu Asp Ser Asn Tyr Asn 485 490 495 Arg Val Ile Ile Met Thr Asp Ala Asp Thr Asp Gly Ala His Ile Gln 500 505 510 Val Leu Leu Leu Thr Phe Phe Phe Lys Tyr Met Lys Pro Leu Val Gln 515 520 525 Ala Gly Arg Val Phe Ile Ala Leu Pro Pro Leu Tyr Lys Leu Glu Lys 530 535 540 Gly Lys Gly Lys Thr Lys Arg Val Glu Tyr Ala Trp Thr Asp Glu Glu 545 550 555 560 Leu Asn Lys Leu Gln Lys Glu Leu Gly Lys Gly Phe Thr Leu Gln Arg 565 570 575 Tyr Lys Gly Leu Gly Glu Met Asn Pro Glu Gln Leu Trp Glu Thr Thr 580 585 590 Met Asn Pro Glu Thr Arg Thr Leu Ile Arg Val Gln Val Glu Asp Glu 595 600 605 Val Arg Ser Ser Lys Arg Val Thr Thr Leu Met Gly Asp Lys Val Gln 610 615 620 Pro Arg Arg Glu Trp Ile Glu Lys His Val Glu Phe Gly Met Gln Glu 625 630 635 640 Asp Gln Ser Ile Leu Asp Asn Ser Glu Val Gln Val Leu Glu Asn Asp 645 650 655 Gln Phe Asp Glu Glu Glu Ile 660 1992 base pairs nucleic acid single linear cDNA 6 ATGAATAAAC AAAATAATTA TTCAGATGAT TCAATACAGG TTTTAGAGGG GTTAGAAGCA 60 GTTCGTAAAA GACCTGGTAT GTATATTGGA TCAACTGATA AACGGGGATT ACATCATCTA 120 GTATATGAAA TTGTCGATAA CTCCGTCGAT GAAGTATTGA ATGGTTACGG TAACGAAATA 180 GATGTAACAA TTAATAAAGA TGGTAGTATT TCTATAGAAG ATAATGGACG TGGTATGCCA 240 ACAGGTATAC ATAAATCAGG TAAACCGACA GTCGAAGTTA TCTTTACTGT TTTACATGCA 300 GGAGGTAAAT TTGGACAAGG TGGCTATAAA ACTTCAGGTG GTCTTCACGG CGTTGGTGCT 360 TCAGTGGTAA ATGCATTGAG TGAATGGCTT GAAGTTGAAA TCCATCGAGA TGGTAATATA 420 TATCATCAAA GTTTTAAAAA CGGTGGTTCG CCATCTTCAG GTTTAGTGAA AAAAGGTAAA 480 ACTAAGAAAA CAGGTACCAA AGTAACATTT AAACCTGATG ACACAATTTT TAAAGCATCT 540 ACATCATTTA ATTTTGATGT TTTAAGTGAA CGACTACAAG AGTCTGCGTT CTTATTGAAA 600 AATTTAAAAA TAACGCTTAA TGATTTACGC AGTGGTAAAG AGCGTCAAGA GCATTACCAT 660 TATGAAGAAG GAATCAAAGA GTTTGTTAGT TATGTCAATG AAGGAAAAGA AGTTTTGCAT 720 GACGTGGCTA CATTTTCAGG TGAAGCAAAT GGTATAGAGG TAGACGTAGC TTTCCAATAT 780 AATGATCAAT ATTCAGAAAG TATTTTAAGT TTTGTAAATA ATGTACGTAC TAAAGATGGT 840 GGTACACATG AAGTTGGTTT TAAAACAGCA ATGACACGCG TATTTAATGA TTATGCACGT 900 CGTATTAATG AACTTAAAAC AAAAGATAAA AACTTAGATG GTAATGATAT TCGTGAAGGT 960 TTAACAGCTG TTGTGTCTGT TCGTATTCCA GAAGAATTAT TGCAATTTGA AGGACAAACG 1020 AAATCTAAAT TGGGTACTTC TGAAGCTAGA AGTGCTGTTG ATTCAGTTGT TGCAGACAAA 1080 TTGCCATTCT ATTTAGAAGA AAAAGGACAA TTGTCTAAAT CACTTGTGAA AAAAGCGATT 1140 AAAGCACAAC AAGCAAGGGA AGCTGCACGT AAAGCTCGTG AAGATGCTCG TTCAGGTAAG 1200 AAAAACAAGC GTAAAGACAC TTTGCTATCT GGTAAATTAA CACCTGCACA AAGTAAAAAC 1260 ACTGAAAAAA ATGAATTGTA TTTAGTCGAA GGTGATTCTG CGGGAGGTTC AGCAAAACTT 1320 GGACGAGACC GCAAATTCCA AGCGATATTA CCATTACGTG GTAAGGTAAT TAATACAGAG 1380 AAAGCACGTC TAGAAGATAT TTTTAAAAAT GAAGAAATTA ATACAATTAT CCACACAATC 1440 GGGGCAGGCG TTGGTACTGA CTTTAAAATT GAAGATAGTA ATTATAATCG TGTAATTATT 1500 ATGACTGATG CTGATACTGA TGGTGCGCAT ATTCAAGTGC TATTGTTAAC ATTCTTCTTC 1560 AAATATATGA AACCGCTTGT TCAAGCAGGT CGTGTATTTA TTGCTTTACC TCCACTTTAT 1620 AAATTGGAAA AAGGTAAAGG CAAAACAAAG CGAGTTGAAT ACGCTTGGAC AGACGAAGAG 1680 CTTAATAAAT TGCAAAAAGA ACTTGGTAAA GGCTTCACGT TACAACGTTA CAAAGGTTTG 1740 GGTGAAATGA ACCCTGAACA ATTATGGGAA ACGACGATGA ACCCAGAAAC ACGAACTTTA 1800 ATTCGTGTAC AAGTTGAAGA TGAAGTGCGT TCATCTAAAC GTGTAACAAC ATTAATGGGT 1860 GACAAAGTAC AACCTAGACG TGAATGGATT GAAAAGCATG TTGAGTTTGG TATGCAAGAG 1920 GACCAAAGTA TTTTAGATAA TTCTGAAGTA CAAGTGCTTG AAAATGATCA ATTTGATGAG 1980 GAGGAAATCT AG 1992 30 base pairs nucleic acid single linear cDNA 7 GCGCGAATTC GATGGWYTWA AACCWGTWCA 30 31 base pairs nucleic acid single linear cDNA 8 CGCGAAGCTT TTCWGTATAW CKCATWGCWG C 31 29 base pairs nucleic acid single linear cDNA 9 GCGCGAATTC TWCATGCWGG WGGWAAATT 29 31 base pairs nucleic acid single linear cDNA 10 CGCGAAGCTT WCCWCCWGCW GAATCWCCTT C 31 7 amino acids amino acid single linear peptide 11 Ala Ala Met Arg Tyr Thr Glu 1 5 7 amino acids amino acid single linear peptide 12 Tyr His Pro His Gly Asp Ser 1 5 29 base pairs nucleic acid single linear cDNA 13 GGCGGATCCC ATATGGCTGA ATTACCTCA 29 29 base pairs nucleic acid single linear cDNA 14 GGCGGAATTC GACGGCTCTC TTTCATTAC 29 35 base pairs nucleic acid single linear cDNA 15 GGCCGGATCC CATATGAGTG AAATAATTCA AGATT 35 32 base pairs nucleic acid single linear cDNA 16 GGCCGAATTC TAATAATTAA CTGTTTACGT CC 32 32 base pairs nucleic acid single linear cDNA 17 GGCCGAGCTC CAATTCTTCT TTTATGACAT TC 32 

1. Nucleotide sequence encoding a subunit of topoisomerase IV of Staphylococcus aureus.
 2. Nucleotide sequence characterized in that it is chosen from: (a) all or part of the grlA (SEQ ID No. 2) or grlB (SEQ ID No. 3) genes, (b) the sequences hybridizing with all or part of the (a) genes and encoding a subunit of a topoisomerase IV, and (c) the sequences derived from the (a) and (b) sequences because of the degeneracy of the genetic code.
 3. Nucleotide sequence according to claim 1 or 2, characterized in that it is the grlA gene (SEQ ID No. 2).
 4. Nucleotide sequence according to claim 1 or 2, characterized in that it is the grlB gene (SEQ ID No. 3).
 5. Nucleotide sequence according to claim 1 or 2, characterized in that it is the grlA gene having a mutation leading to a resistance towards molecules of the quinolone family.
 6. Nucleotide sequence according to claim 5, characterized in that it is the grlA gene having a base A as a substitution for a base C at position 2270 of SEQ ID No.
 2. 7. Recombinant DNA comprising a nucleotide sequence according to on of claims 1 to
 6. 8. Autonomously replicating and/or integrative expression vector characterized in that it comprises a nucleotide sequence according to one of claims 1 to
 6. 9. Recombinant cell containing a nucleotide sequence according to one of claims 1 to 6, a recombinant DNA according to claim 7 and/or an expression vector according to claim
 8. 10. Cell according to claim 8, characterized in that it is preferably a bacterium.
 11. Polypeptide resulting from the expression of at least one sequence according to one of claims 1 to
 6. 12. Polypeptide comprising all or part of the polypeptide GrlA (SEQ ID No. 2), of the polypeptide GrlB (SEQ ID No. 3) or of a derivative thereof.
 13. Polypeptide according to claim 11 or 12, characterized in that it is the polypeptide GrlA (SEQ ID No. 2).
 14. Polypeptide according to claim 11 or 12, characterized in that it is the polypeptide GrlB (SEQ ID No. 3).
 15. Polypeptide according to claim 11 or 12, characterized in that it is the polypeptide GrlA_((Ser-80→Tyr)).
 16. Process for the production of a polypeptide according to one of claims 11 to 15, charact riz d in that a r combinant cell according to claim 9 or 10 is cultur d and th polypeptid produced is recovered.
 17. Isolated topoisomerase IV characterized in that it is capable of being obtained from the expression of all or part of the grlA gene (SEQ ID No. 2) and of all or part of the grlB gene (SEQ ID No. 3), or of their respective derivatives as defined in b) and c) of claim
 2. 18. Isolated topoisomerase IV according to claim 17, characterized in that it is derived from the expression of all or part of the grlA gene (SEQ ID No. 2) and of all or part of the grlB gene (SEQ ID No. 3).
 19. Isolated topoisomerase IV, characterized in that it has the behaviour of a primary target towards the fluoroquinolones.
 20. Isolated topoisomerase IV according to one of the preceding claims, characterized in that it is topoisomerase IV of Staphylococcus aureus.
 21. Use of a topoisomerase IV according to one of claims 17 to 20 to target biologically active products.
 22. Use of a topoisomerase IV according to one of claims 17 to 20 to search for products inhibiting th ATP-d p ndent DNA r laxing reaction.
 23. Use of a topoisomeras IV according to one of claims 17 to 20 for identifying products inhibiting the reaction of decatanation of catenanes of DNA. 